Details for 4pjc

Click on any of the tabs below to see the detailed information about the structure.

Structure visualisation

Display options:
Cartoon model
Spacefill model
Wire model
Ball&stick model
Default colouring
Color by B-factor
Color by chain
Color by sec. structure
Color by element
Spin: on off

Structure information

Structure of Human Mr1-5-Op-Ru in complex with Human Mait C-a11 TCR

Item	Info
PDB	4pjc
Organism	HOMO SAPIENS
Method	X-RAY DIFFRACTION
Resolution	2.5Å
Number of TCRs	2

Paired chains information

This PDB has 2 TCR(s).

F / E

TCR Details:

Item	Info
VB chain	F
VA chain	E
VB IMGT details	TRBV6/TRBJ1
VA IMGT details	TRAV1/TRAJ33
Species	human

Antigen Details:

Item	Info
Antigen Chain	A \| A
Antigen Type	Unknown
Antigen Organism	HOMO SAPIENS
Antigen name	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL; 1-DEOXY-1-({2,6-DIOXO-5-[(E)-(2-OXOPROPYLIDENE)AMINO]-1,2,3,6-TETRAHYDROPYRIMIDIN-4-YL}AMINO)-D-RIBITOL
Antigen residue	B3P \| 2LJ

MHC details:

Item	Info
MHC Chain	A \| B
MHC Type	MR1
MHC Species	human
MHC IMGT details	MR1*01

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

B1	B2	B3	B4	B5	B6	B7	B8
N	A	G	V	T	Q	T	P
B9	B10	B11	B12	B13	B14	B15	B16
K	F	Q	V	L	K	T	G
B17	B18	B19	B20	B21	B22	B23	B24
Q	S	M	T	L	Q	C	A
B25	B26	B27	B28	B29	B37	B38	B39
Q	D	M	N	H	N	S	M
B40	B41	B42	B43	B44	B45	B46	B47
Y	W	Y	R	Q	D	P	G
B48	B49	B50	B51	B52	B53	B54	B55
M	G	L	R	L	I	Y	Y
B56	B57	B58	B63	B64	B65	B66	B67
S	A	S	E	G	T	T	D
B68	B69	B70	B71	B72	B74	B75	B76
K	G	E	V	P	N	G	Y
B77	B78	B79	B80	B81	B83	B84	B85
N	V	S	R	L	N	K	R
B86	B87	B88	B89	B90	B91	B92	B93
E	F	S	L	R	L	E	S
B94	B95	B96	B97	B98	B99	B100	B101
A	A	P	S	Q	T	S	V
B102	B103	B104	B105	B106	B107	B108	B109
Y	F	C	A	S	S	A	A
B110	B111	B112	B113	B114	B115	B116	B117
V	E	G	G	N	T	I	Y
B118	B119	B120	B121	B122	B123	B124	B125
F	G	E	G	S	R	L	T
B126	B127
V	L

FASTA file

A1	A2	A3	A4	A5	A6	A8	A9
G	Q	N	I	D	Q	P	T
A10	A11	A12	A13	A14	A15	A16	A17
E	M	T	A	T	E	G	A
A18	A19	A20	A21	A22	A23	A24	A25
I	V	Q	I	N	C	T	Y
A26	A27	A28	A29	A36	A37	A38	A39
Q	T	S	G	F	N	G	L
A40	A41	A42	A43	A44	A45	A46	A47
F	W	Y	Q	Q	H	A	G
A48	A49	A50	A51	A52	A53	A54	A55
E	A	P	T	F	L	S	Y
A56	A57	A58	A63	A64	A65	A66	A67
N	V	L	D	G	L	E	E
A68	A74	A75	A76	A77	A78	A79	A80
K	G	R	F	S	S	F	L
A81	A82	A83	A84	A85	A86	A87	A88
S	R	S	K	G	Y	S	Y
A89	A90	A91	A92	A93	A94	A95	A96
L	L	L	K	E	L	Q	M
A97	A98	A99	A100	A101	A102	A103	A104
K	D	S	A	S	Y	L	C
A105	A106	A107	A108	A109	A113	A114	A115
A	V	R	D	S	N	Y	Q
A116	A117	A118	A119	A120	A121	A122	A123
L	I	W	G	A	G	T	K
A124	A125	A126	A127	A128
L	I	I	K	P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSAAVEGGNTIY	None	13
CDRB2	SASEGT	None	6
CDRB1	MNHNS	None	5
CDRA3	AVRDSNYQLI	None	10
CDRA2	NVLDGL	None	6
CDRA1	TSGFNG	A1-6-F	6

Orientation and docking angles:

Angle	Value
BC2	102.47°
BC1	72.37°
BA	-59.74°
AC2	79.13°
AC1	123.72°
dc	16.65Å
Docking angle	59.92°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
7ow6_ED	102.49°	72.80°	-58.89°	79.33°	124.44°	16.95Å	1.2
6pug_ED	103.58°	72.88°	-60.35°	80.20°	123.58°	16.68Å	1.7
3rev_BA	101.29°	71.79°	-60.65°	78.74°	124.05°	16.31Å	1.7
4pji_HG	102.90°	73.29°	-61.00°	79.63°	123.90°	16.81Å	1.7
4pja_FE	102.90°	72.45°	-60.92°	80.29°	123.91°	16.77Å	1.7

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
1cfq_BA	106.86°	67.47°	-56.63°	80.83°	119.58°	16.37Å	8.5
1nma_HL	109.88°	72.48°	-61.03°	81.63°	120.29°	16.40Å	8.6
4hxb_HL	109.66°	72.24°	-59.19°	82.14°	119.35°	16.41Å	9.0
3mo1_BA	109.77°	73.00°	-58.46°	81.03°	119.12°	16.26Å	9.0
1ghf_HL	110.63°	71.68°	-61.52°	81.98°	122.12°	16.05Å	9.0

H / G

TCR Details:

Item	Info
VB chain	H
VA chain	G
VB IMGT details	TRBV6/TRBJ1
VA IMGT details	TRAV1/TRAJ33
Species	human

Antigen Details:

Item	Info
Antigen Chain	C \| C
Antigen Type	Unknown
Antigen Organism	HOMO SAPIENS
Antigen name	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL; 1-DEOXY-1-({2,6-DIOXO-5-[(E)-(2-OXOPROPYLIDENE)AMINO]-1,2,3,6-TETRAHYDROPYRIMIDIN-4-YL}AMINO)-D-RIBITOL
Antigen residue	B3P \| 2LJ

MHC details:

Item	Info
MHC Chain	C \| D
MHC Type	MR1
MHC Species	human
MHC IMGT details	MR1*01

Numbered sequence

Chain type

Chain ID

FASTA/Annotation file

IMGT numbered sequence (Framework/CDR)

FASTA file

B1	B2	B3	B4	B5	B6	B7	B8
N	A	G	V	T	Q	T	P
B9	B10	B11	B12	B13	B14	B15	B16
K	F	Q	V	L	K	T	G
B17	B18	B19	B20	B21	B22	B23	B24
Q	S	M	T	L	Q	C	A
B25	B26	B27	B28	B29	B37	B38	B39
Q	D	M	N	H	N	S	M
B40	B41	B42	B43	B44	B45	B46	B47
Y	W	Y	R	Q	D	P	G
B48	B49	B50	B51	B52	B53	B54	B55
M	G	L	R	L	I	Y	Y
B56	B57	B58	B63	B64	B65	B66	B67
S	A	S	E	G	T	T	D
B68	B69	B70	B71	B72	B74	B75	B76
K	G	E	V	P	N	G	Y
B77	B78	B79	B80	B81	B83	B84	B85
N	V	S	R	L	N	K	R
B86	B87	B88	B89	B90	B91	B92	B93
E	F	S	L	R	L	E	S
B94	B95	B96	B97	B98	B99	B100	B101
A	A	P	S	Q	T	S	V
B102	B103	B104	B105	B106	B107	B108	B109
Y	F	C	A	S	S	A	A
B110	B111	B112	B113	B114	B115	B116	B117
V	E	G	G	N	T	I	Y
B118	B119	B120	B121	B122	B123	B124	B125
F	G	E	G	S	R	L	T
B126	B127
V	L

FASTA file

A1	A2	A3	A4	A5	A6	A8	A9
G	Q	N	I	D	Q	P	T
A10	A11	A12	A13	A14	A15	A16	A17
E	M	T	A	T	E	G	A
A18	A19	A20	A21	A22	A23	A24	A25
I	V	Q	I	N	C	T	Y
A26	A27	A28	A29	A36	A37	A38	A39
Q	T	S	G	F	N	G	L
A40	A41	A42	A43	A44	A45	A46	A47
F	W	Y	Q	Q	H	A	G
A48	A49	A50	A51	A52	A53	A54	A55
E	A	P	T	F	L	S	Y
A56	A57	A58	A63	A64	A65	A66	A67
N	V	L	D	G	L	E	E
A68	A74	A75	A76	A77	A78	A79	A80
K	G	R	F	S	S	F	L
A81	A82	A83	A84	A85	A86	A87	A88
S	R	S	K	G	Y	S	Y
A89	A90	A91	A92	A93	A94	A95	A96
L	L	L	K	E	L	Q	M
A97	A98	A99	A100	A101	A102	A103	A104
K	D	S	A	S	Y	L	C
A105	A106	A107	A108	A109	A113	A114	A115
A	V	R	D	S	N	Y	Q
A116	A117	A118	A119	A120	A121	A122	A123
L	I	W	G	A	G	T	K
A124	A125	A126	A127	A128
L	I	I	K	P

CDR Sequences:

Loop	Sequence	Predicted canonical form	CDR Length
CDRB3	ASSAAVEGGNTIY	None	13
CDRB2	SASEGT	None	6
CDRB1	MNHNS	None	5
CDRA3	AVRDSNYQLI	None	10
CDRA2	NVLDGL	None	6
CDRA1	TSGFNG	A1-6-F	6

Orientation and docking angles:

Angle	Value
BC2	103.15°
BC1	72.48°
BA	-61.53°
AC2	78.37°
AC1	123.38°
dc	16.57Å
Docking angle	61.48°

TCRs with similar orientations:

TCR PDB	BC2	BC1	BA	AC2	AC1	dc	TRangle Distance
3qh3_DC	103.38°	73.21°	-61.36°	77.35°	122.64°	16.34Å	1.5
8i5c_nm	104.21°	72.97°	-60.48°	78.59°	123.50°	16.53Å	1.6
6pvc_FE	103.37°	72.87°	-61.55°	79.93°	123.71°	16.68Å	1.7
4pjf_HG	103.12°	73.06°	-61.65°	79.97°	123.64°	16.66Å	1.7
4pji_HG	102.90°	73.29°	-61.00°	79.63°	123.90°	16.81Å	1.7

Antibodies with similar orientations:

Antibody PDB	HC2	HC1	HL	LC2	LC1	dc	ABangle Distance
4yfl_FI	106.92°	71.36°	-64.48°	73.60°	120.95°	15.85Å	7.3
4dcq_BA	108.30°	73.42°	-64.76°	82.94°	120.98°	16.23Å	8.0
1nmc_HL	110.09°	71.80°	-64.06°	80.19°	120.88°	16.16Å	8.0
1nma_HL	109.88°	72.48°	-61.03°	81.63°	120.29°	16.40Å	8.1
3s96_AB	107.61°	73.57°	-66.51°	82.70°	120.78°	16.43Å	8.5

Available downloads

Additional links and files for download: see help for more details.

Item	Link
IMGT-numbered structure	Link
Non-annotated structure from the PDB	Link
Summary file for this TCR	Link
Link in the PDB	Link